Genes influencing phage host range in Staphylococcus aureus on a species-wide scale

Abstract

Staphylococcus aureus is a human pathogen that causes serious diseases ranging from skin infections to septic shock. Bacteriophages (“‘phages”‘) are both natural killers of S. aureus, offering therapeutic possibilities, as well as important vectors of horizontal gene transfer in the species. Here, we used high-throughput approaches to understand the genetic basis of strain-to-strain variation in sensitivity to phages, which defines the host range. We screened 259 diverse S. aureus strains covering more than 40 sequence types for sensitivity to eight phages, which were representatives of the three phage classes that infect the species. The phages were variable in host range, each infecting between 73 and 257 strains. Using genome-wide association approaches, we identified putative loci that affect host range and validated their function using USA300 transposon knockouts. In addition to rediscovering known host range determinants, we found several genes previously unreported genes affecting phage infection, including trpA, phoR, isdB, sodM, fmtC, and relA. We used the data from our host range matrix to develop predictive models that achieved between 40 and 95% accuracy. This work illustrates the complexity of the genetic basis for phage susceptibility in S. aureus but also shows that with more data, we may be able to understand much of the variation. With a knowledge of host range determination, we can rationally design phage therapy cocktails that target the broadest host range of S. aureus strains and address basic questions regarding phage-host interactions, such as the impact of phage on S. aureus evolution.ImportanceStaphylococcus aureus is a widespread, hospital- and community-acquired pathogen, many strains of which are antibiotic resistant. It causes diverse diseases ranging from local to systemic infection and affects both the skin and many internal organs, including the heart, lungs, bones, and brain. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent. One alternative therapy to antibiotics is phage therapy, in which viruses specific to infecting bacteria clear infection. In this work, we identify and validate S. aureus genes that influence phage host range - the number of strains a phage can infect and kill - by testing strains representative of the diversity of the S. aureus species for phage host range and associating strain’s genome sequences with host range. These findings together improve our understanding of how phage therapy works in the bacterium and improve prediction of phage therapy efficacy based on the infecting strain’s predicted host range.

Bacterial Targets of Antibiotics in Methicillin-Resistant Staphylococcus aureus

“…The use of antivirulence compounds may not exert the selective pressure on bacteria that leads to the emergence of antimicrobial resistance [ 80 ]. Furthermore, phage therapy, the use of bacteriophage viruses that kill specific bacteria through lytic activity, is being considered as there is little or no human toxicity from such viruses, and there is a highly diverse selection of natural phages available, suggesting that complete resistance would be difficult to evolve [ 81 , 82 ]. For instance, the bacteriophage lysin PlySs2 is undergoing Phase 3 clinical trials as an addition to standard-of-care antibiotics for the treatment of patients with S. aureus bacteremia, including endocarditis ( , accessed on 12 March 2021).…”

Species-scale genomic analysis of S. aureus genes influencing phage host range and their relationships to virulence and antibiotic resistance genes

“…We next asked whether phage resistance gene presence could explain two relevant phenotypes -empirical resistance to infection against 8 phages in 259 diverse S. aureus strains determined by laboratory assays (35), and variation in the total number of accessory genes in the set of completely assembled S. aureus genomes. While no phage resistance gene categories correlated with measured virulent (p002y and pyo) phage resistance, all phage resistance genes, biosynthesis genes, and superinfection immunity genes (a subset of biosynthesis genes responsible for lysogens repressing superinfecting phages) (36) correlated positively with temperate (p11 and p0040) phage resistance (Figure 6).…”

“…Non-extended-core resistance gene correlation analyses with empirical phage resistance and accessory genome content We examined the relationship between non-extended-core phage resistance genes and 1) experimentally measured phage resistance phenotypes, 2) accessory genome content, and 3) non-extended-core antibiotic resistance or virulence gene content. We used genomes of previously resistance-phenotyped strains from our S. aureus genome-wide host range study (35) and genomes of all completely assembled S. aureus genomes (26) to address the first and second objectives, respectively (the third we addressed with both sets). Antibiotic resistance genes searched were previously identified in S. aureus genomes (68), whereas virulence genes searched were the Virulence Factor Database (VFDB) set (69).…”